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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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pip install in conda does not allow for download #264

Open da-i opened 2 years ago

da-i commented 2 years ago

Hi Openvax,

I've created a new conda env and installed via pip as suggested by the instructions. If i run pyensembl install --species human I get an error (see below), due to the fact the the requested url is not responsive. (eg its not working with curl or wget either).

I think this is due to the fact that the code refers to ftp://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/cdna/Homo_sapiens.G RCh38.cdna.all.fa.gz

whilst wget works on: http://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/cdna/Homo_sapiens.G RCh38.cdna.all.fa.gz.

$ pyensembl install --species human                                                                               
2022-04-20 13:51:09,574 - pyensembl.shell - INFO - Running 'install' for EnsemblRelease(release=106, species='homo_sapiens')                  
2022-04-20 13:51:09,574 - pyensembl.download_cache - INFO - Fetching /home/dami/.cache/pyensembl/GRCh38/ensembl106/Homo_sapiens.GRCh38.106.gtf
.gz from URL ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz                                            
2022-04-20 13:51:09,574 - datacache.download - INFO - Downloading ftp://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.1
06.gtf.gz to /home/dami/.cache/pyensembl/GRCh38/ensembl106/Homo_sapiens.GRCh38.106.gtf.gz                                                     
Traceback (most recent call last):                                                                                                            
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 1563, in ftp_open                                      
    fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)                                                                        
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 1584, in connect_ftp                                   
    return ftpwrapper(user, passwd, host, port, dirs, timeout,                                                                                
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 2405, in __init__                                      
    self.init()                                                                                                                               
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 2414, in init                                          
    self.ftp.connect(self.host, self.port, self.timeout)                                                                                      
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/ftplib.py", line 158, in connect                                                
    self.sock = socket.create_connection((self.host, self.port), self.timeout,                                                                
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/socket.py", line 844, in create_connection                                      
    raise err                                                                                                                                 
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/socket.py", line 832, in create_connection                                      
    sock.connect(sa)                                                                                                                          
TimeoutError: [Errno 110] Connection timed out                                                                                                

During handling of the above exception, another exception occurred:                                                                           

Traceback (most recent call last):                                                                                                            
  File "/home/dami/miniconda3/envs/dataanalysis/bin/pyensembl", line 8, in <module>                                                           
    sys.exit(run())                                                    
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/shell.py", line 255, in run
    genome.download(overwrite=args.overwrite)                         
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/genome.py", line 266, in download
    self._set_local_paths(download_if_missing=True, overwrite=overwrite)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/genome.py", line 222, in _set_local_paths
    self.gtf_path = self._get_gtf_path(
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/genome.py", line 184, in _get_gtf_path
    return self._get_cached_path(                                      
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/genome.py", line 177, in _get_cached_path
    return self.download_cache.local_path_or_install_error(                                                                                   
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/download_cache.py", line 309, in local_path_or_install_e
rror         
    return self.download_or_copy_if_necessary(                                                                                                
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/download_cache.py", line 285, in download_or_copy_if_nec
essary                                                                                                                                        
    return self._download_if_necessary(                                                                                                       
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/pyensembl/download_cache.py", line 231, in _download_if_necessary
    datacache.download._download_and_decompress_if_necessary(                                                                                 
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/datacache/download.py", line 105, in _download_and_decompress_if_n
ecessary                                                                                                                                      
    tmp_path = _download_to_temp_file(                                                                                                        
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/datacache/download.py", line 68, in _download_to_temp_file
    download_using_python()                                                                                                                   
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/datacache/download.py", line 65, in download_using_python
    _download(download_url, timeout=timeout))                                                                                                 
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/site-packages/datacache/download.py", line 42, in _download
    response = urllib.request.urlopen(req, data=None, timeout=timeout)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 214, in urlopen
    return opener.open(url, data, timeout)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 517, in open
    response = self._open(req, data)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 534, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 494, in _call_chain
    result = func(*args)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 1581, in ftp_open
    raise exc.with_traceback(sys.exc_info()[2])
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 1563, in ftp_open
    fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 1584, in connect_ftp
    return ftpwrapper(user, passwd, host, port, dirs, timeout,
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 2405, in __init__
    self.init()
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/urllib/request.py", line 2414, in init
    self.ftp.connect(self.host, self.port, self.timeout)
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/ftplib.py", line 158, in connect
    self.sock = socket.create_connection((self.host, self.port), self.timeout,
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/socket.py", line 844, in create_connection
    raise err
  File "/home/dami/miniconda3/envs/dataanalysis/lib/python3.9/socket.py", line 832, in create_connection
    sock.connect(sa)
urllib.error.URLError: <urlopen error ftp error: TimeoutError(110, 'Connection timed out')>

Let me know if the issue is not clear enough

da-i commented 2 years ago

Updating to ENSEMBL_FTP_SERVER = "http://ftp.ensembl.org" in pyensembl/ensembl_url_templates.py resolves the issue